- Introduction to single-cell RNA-seq
- Quality control and normalization
- Survey of downstream analysis methodology
July 6, 2019
image source: http://carbonandsilicon.net/rblogging/2018/02/27/UMAP_plots
Andrews & Hemburg 2018 (https://doi.org/10.1016/j.mam.2017.07.002)
Risso et al 2018 (https://doi.org/10.1371/journal.pcbi.1006378)
Korthauer et al 2016 (https://doi.org/10.1186/s13059-016-1077-y)
Korthauer et al 2016 (https://doi.org/10.1186/s13059-016-1077-y)
Soneson & Robinson 2018 (https://doi-org.ezp-prod1.hul.harvard.edu/10.1038/nmeth.4612)
## <27998 x 1306127> HDF5Matrix object of type "integer": ## [,1] [,2] [,3] [,4] ... [,1306124] ## [1,] 0 0 0 0 . 0 ## [2,] 0 0 0 0 . 0 ## [3,] 0 0 0 0 . 0 ## [4,] 0 0 0 0 . 0 ## [5,] 0 0 0 0 . 0 ## ... . . . . . . ## [27994,] 0 0 0 0 . 0 ## [27995,] 1 0 0 2 . 0 ## [27996,] 0 0 0 0 . 0 ## [27997,] 0 0 0 0 . 0 ## [27998,] 0 0 0 0 . 0 ## [,1306125] [,1306126] [,1306127] ## [1,] 0 0 0 ## [2,] 0 0 0 ## [3,] 0 0 0 ## [4,] 0 0 0 ## [5,] 0 0 0 ## ... . . . ## [27994,] 0 0 0 ## [27995,] 1 0 0 ## [27996,] 0 0 0 ## [27997,] 0 0 0 ## [27998,] 0 0 0
For a gentle introduction to the nitty gritty details of how the DelayedArray framework works, see the tutorial “Effectively_using_the_DelayedArray_framework_for_users” from the 2019 Bioconductor meeting
For practice using scater and scran with HDF5 files the tutorial “Analysis of Large Single-Cell RNA-Seq Datasets in R/Bioconductor”, also from the 2019 Bioconductor meeting
Zappia, Phipson & Oshlack 2018 (https://doi.org/10.1371/journal.pcbi.1006245)